Maintained by Robin Tecon, microbiologist and postdoctoral researcher at the Swiss Federal Institute of Technology Zürich. This blog is about bacteria (and other microbes) and the scientists who study them.

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Thursday, July 05, 2012

Kingdoms or domains?

I view taxonomy – the classification of organisms – at the same time as the most useless and the most useful science. Useless because we know that all life forms are related to one another, and therefore the categories that we create to separate them are arbitrary (with the exception of the distinction at the species level). Most useful, since naming and organizing things seem necessary if we are to claim any knowledge. And isn't it a true pleasure (I almost dare to write "bliss") to point at a plant, a mushroom or an animal (if the latter doesn't move too fast) and be able to name it?

I learned my share of taxonomy as a student, but I also forgot quite a bunch… At least I remember that I got a good grade at my zoology exam (I had to talk about the subphylum Chelicerata!), based on a course by one of the best professors I ever had, Peter Vogel.

Taxonomy, which is part of Systematics (the study of biological diversity), proposes a hierarchy from the most particular to the most general: Species, Genera, Families, Orders, Classes, Phyla… (In the classic evolutionary taxonomy, classification is mostly based on morphology, while modern molecular systematics compares the sequence of amino acids in proteins or of nucleotides in nucleic acids.) But, what about higher (more global) levels of classification? Five kingdoms

When I was a first year biology student, it was written in my general textbook (Campbell, 1995) that all organisms could be grouped into five kingdoms: Monera (bacteria or prokaryotes), Protists (unicellular eukaryotes and some simple multicellular ones), Plants, Fungi and Animals. That is the classic view. And it is actually valid and serves its purpose very well.

"Five kingdoms" is also the title of a wonderful book by Lynn Margulis and Karlene Schwartz, of which I got a copy (first edition) while visiting the Curious Book Shop in East Lansing last year (great place for second-hand books, don't miss it if you're around!). "An illustrated guide to the phyla of life on Earth" is the subtitle of the book, and it's a perfect description, since it is packed with magnificent photographs and drawings. Focus is on phyla, so groups with only few representative species (for instance, the phylum Placozoa and its unique species Trichoplax adhaerens) are given as much importance as large groups such as Arthropods. A welcome gift to any biologist.

Margulis and Schwartz follow the traditional "five kingdoms" classification with one exception: they replaced the term "Protista" (Protists) by "Protoctista", from the greek words protos (very first) and ktistos (to establish). They consider that the term Protist is connoted with a single-cell organism, which thus excludes organisms such as euglenoids, chrysophytes and diatoms. If I find the reasoning perfectly valid here, I regret that the authors came up with such an ugly name!

Three domains

But my old textbook also mentioned, albeit briefly, a new taxonomic category which would represent one level higher than kingdoms. This new category – called domain – was proposed by Carl Woese based on its study of ribosomal RNA genes. In Woese's view (which is also the current view of the scientific community), the three domains of life are Bacteria, Archaea and Eukarya (I wrote a short post about it). Eukarya, actually, emerged from Bacteria and Archaea ancestors.

So what is it finally, kingdom or domain? Both are meaningful, but it is clear that the five-kingdom explanation overlooks the fundamental difference that exists between Bacteria and Archaea. It does so for a good reason: morphological differences between Bacteria and Archaea are trivial. My personal feeling here is that microbiologists are very aware of this fundamental classification of the living forms, while other biologists, well, they tend to forget about it…

Now, since she is a microbiologist, why is it that Margulis does not acknowledge the three domains classification in her book? It is not because she did not know about Woese's work, since he published it in 1977 and the first edition of Margulis' Five Kindgoms was published in 1982. An explanation can be found in Margulis' book "Symbiotic Planet" (I previously discussed the book). She wrote, p.65:

"In my view, Woese obscures rather than illuminates the critical distinction between prokaryotes and eukaryotes, between symbiogenetic and nonsymbiogenetic life."

And p. 66:

"In Woese's three-domain taxonomy, molecular differences between the two kinds of bacteria are given more importance than the differences between a mushroom and a moose. To me this is ludicrous. […] Bacteriophile though I am, I believe our newly modified two-tiered (Prokarya, Eukarya) five-kingdom scheme, published in 1998, is far superior to the three-domain classification."

(I have to say that I don't see how the 1998 scheme is "modified" in comparison to the 1982 scheme, because both illustrations seem the same to me.)

I am still puzzled that Lynn Margulis, who always was, as she wrote, a great "bacteriophile", did not embrace the three-domain view. The three-domain scheme, I believe, gives the microbes their rightful place in the tree of life! It has to be noted, however, that the latest edition of Margulis' book, published in 2009, has been renamed "Kingdoms and domains"! A concession suggested by the publisher? Not impossible, given that the introduction of the book still reads:

"Although we are deeply indebted to Carl Woese […], we reject the bacteriocentric three-domain scheme on biological, evolutionary and pedagogical grounds."

Despite my reservations on this 'domain vs. kingdom' issue, "Five kingdoms" is a unique book and a warmly recommended read!